cing and genetic manipulations, we can find genetic differences and even identify which mutations matter.  But really opening up the “black box”—understanding how functionally a mutation makes one genotype more fit than another—remains a tough problem for us in most cases.

DSW: The comparison with the Grants’ research is indeed apt. I know that, through collaborations, they are getting at the proximate mechanisms also. Finally, we get to Tinbergen’s “Development” question, which requires understanding how a given trait comes into being during the lifetime of an organism, in addition to the mechanistic basis of the fully developed trait. Does the concept of development make sense in a bacterium such as E. coli? Does your research include Tinbergen’s fourth question?

RL: I guess that depends on definitions.  Since E. coli is a single-celled organism, it doesn’t have development in the usual sense.  But cells do have a life cycle of sorts and lifetimes over which their circumstances change.  Understanding how bacteria get information from their environments and use that information to turn genes on and off has long been a part of microbial genetics, as exemplified by François Jacob and Jacques Monod’s work on the lac operon, which won a Nobel Prize.  That work was also very influential in getting people to think about the role of gene regulation in the development of multicellular organisms.

Thinking about life histories in the context of the LTEE, every day the bacteria are diluted into fresh medium, and each day they experience a series of growth phases that correspond to different physiological states.  There’s a lag phase when the cells are gearing up to start growing again on the renewed resources.  That’s followed by exponential growth, when the cell population is growing at its maximum rate for the conditions.  But as the cell numbers increase, they draw down the glucose and, once it’s depleted, they enter what’s called stationary phase.  They don’t die appreciably during stationary phase, at least not when it’s fairly brief like in the LTEE.  Anyhow, we’ve found that the bacteria not only evolved faster exponential growth, they’ve also substantially reduced the duration of the lag phase prior to growth.  So they’ve evolved to respond faster to the transition into fresh medium or perhaps to end up in stationary phase better prepared for that coming transition.

Also, all 12 lines make cells that are much larger than those of the ancestral strain.  That was another surprise and seems counterintuitive in a couple of respects.  First, larger organisms usually grow more slowly and have longer generation times than smaller ones.  Think of elephants versus mice, for example.  Yet in the LTEE we’ve evolved cells that are larger, grow faster, and have shorter generation times than their ancestor.  Second, from a functional perspective, if you had asked me at the start of the LTEE whether the bacterial cells would evolve to become smaller or larger, I’d have predicted smaller because that would give them a higher ratio of surface area to volume, which would seem advantageous in acquiring resources.  But the bacteria clearly had a different opinion, so to say, because they’ve become much larger—and in most cases they’re a bit rounder and less rod-shaped, which further reduces the area-to-volume ratio.  So what’s going on?  Once again, I don’t know, but I think the bigger cells might have an advantage because they are bigger sponges.  Although their surface-to-volume ratio is less favorable, each big cell has more total surface area than each small cell.  In the LTEE there’s a race every day to get as much of the glucose as possible before it runs out.  A larger cell can hold onto the glucose molecules that it gobbles up and pass them on to its daughter cells.  So maybe the larger cells, while appearing inelegant from an engineering standpoint, are a maternal investment in the kids’ future.  That would be pretty cool.

DSW: Hmmm. Parental care in bacteria! So far I have been portraying your research as confirming the basic elements of evolutionary theory, as if all of your results could be predicted beforehand. However, I know that empirical research usually also results in surprises that no one could have predicted before hand. You’ve already mentioned the ability to digest citrate, which might be like us evolving the ability to digest hay. What are some other big surprises?

RL:  The results are certainly consistent with the basic elements of evolutionary theory.  Those elements are pretty darn simple and well understood: mutation and recombination generate heritable variation, and selection and drift affect the fate of variants.  (Although the bacteria in the LTEE don’t have recombination in the sense of genetic exchange.)  Yet from “this view of life”—to echo Darwin’s words and your site’s name—“endless forms most beautiful and most wonderful have been, and are being, evolved.”

It might seem depressing, from the vantage of scientific discovery, to say that all of evolution comes down to a few basic processes.  But physics, too, boils down to just a few fundamental forces—gravity, electromagnetism, and strong and weak nuclear interactions.  Yet together they gave rise to the elements and chemistry as well as to stars, galaxies, and solar systems.  In the same vein, the core processes of organic evolution produce fascinating higher-level dynamics and phenomena like speciation and cooperation.

Now back to some surprises from the LTEE that could not have been predicted, or at least weren’t what I expected at the outset.  I’m tempted to say that, beyond the fact that the bacteria got more fit, almost everything has been unpredictable—certainly the details of what changed genetically, but also many of the interesting phenotypic changes.  I’ve mentioned several of them: the evolution of higher mutation rates, the larger cells, the stable polymorphism despite the simplicity of the environment, and the evolution of the ability to use citrate.  On that last point, perhaps the surprising thing has gone from “Wow, it happened!” to “Gee, why is it so difficult that only one population has figured it out even after 60,000 generations?”

At a more abstract level, I’ve been surprised by two other outcomes.  When I started the LTEE, I thought the replicate populations would follow very different paths and that their divergence would be obvious just from looking at the fitness trajectories.  In the metaphor of Sewall Wright, I imagined the adaptive landscape was rugged with multiple peaks, such that the populations would reach different fitness levels based on the luck o5captionf their early mutational steps.  As I said earlier, it is the case that the longer we watch the LTEE, the more we see that the populations have diverged in terms of both their fitness and genetics.  Still, I’ve been surprised that the fitness trajectories are so similar and that there’s been so much genetic parallelism.

Even more surprising to me, I thought the fitness trajectories would level off—that the bacteria would reach an asymptote, or upper limit, beyond which they couldn’t grow any faster.  We’ve seen the rate of improvement in fitness slow over time, but it slows down in a way that fits a power-law relation, which has no upper limit but instead tracks the logarithm of time.  Not only does the power-law model fit the data much better than a model with an asymptote, we’ve shown that it is predictive.  For example, given just 5000 generations of fitness data, the power-law model predicts the trajectory very well out to 50,000 generations.  Now there may well be some ultimate limit, but even if we extrapolate the trajectory to millions of generations, the implied growth rates and fitness effects that would be subject to selection are biologically reasonable and plausible.  Evolutionary biologists have usually thought of changing environments, including coevolution with other species, as what keeps evolution going.  Of course, changing environments are a huge part of nature and critically important for understanding evolution.  But our results also suggest that evolution can keep discovering ways to improve even in a constant world.  I hope the LTEE will continue for many more generations—and here I mean generations of scientists—to see whether this prediction holds up and to see what other surprises emerge from the potent mix of bacteria, time, and human ingenuity.

DSW: This has been a blast! I think that our conversation has done a good job describing evolutionary theory as a workaday toolkit–capable of producing a cathedral of knowledge.

RL: Yes, it’s been great fun!  And you’ve made me think about how our work relates to Tinbergen’s framework for understanding evolution.